use the "sort" command after adding atoms:
PyMOL> h_add 1ycr
Matthew Baumgartner wrote, On 03/26/13 13:59:
> When I fetch a new structure (1YCR, for example) then run 'h_add 1ycr'
> the hydrogens are added to the structure as expected, but they are put
> in the sequence viewer as their own residue with the same chain.
> This is problematic for several reasons, one is that it breaks
> selections, when I click on a heavy atom of a residue (in residue
> selection mode) only the heavy atoms are selected and not the
> hydrogens. Also, if I save the structure to an pdb file, all of the
> hydrogens for the whole structure are placed at the beginning or the end
> of the structure, which makes them difficult to be interpreted by other
> programs (babel, chimera, namd, etc).
> I am using Pymol 22.214.171.124. (I will be updating to 1.6 soon).
> Any suggestions for settings to change or a workaround (possibly
> involving other programs, if necessary), would be greatly appreciated.